PEWO: a collection of workflows to benchmark phylogenetic placement
| Autor: | Nikolai Romashchenko, Fabio Pardi, Benjamin Linard, Eric Rivals |
|---|---|
| Přispěvatelé: | Méthodes et Algorithmes pour la Bioinformatique (MAB), Laboratoire d'Informatique de Robotique et de Microélectronique de Montpellier (LIRMM), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Institut Français de Bioinformatique (IFB-CORE), Institut National de Recherche en Informatique et en Automatique (Inria)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM) |
| Rok vydání: | 2020 |
| Předmět: |
0106 biological sciences
Statistics and Probability Computer science [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics Phylogenetics and taxonomy 010603 evolutionary biology 01 natural sciences Biochemistry Workflow 03 medical and health sciences Placement Evaluation Molecular Biology Phylogeny 030304 developmental biology 0303 health sciences Genome Phylogenetic tree Data science Computer Science Applications Computational Mathematics Benchmarking Computational Theory and Mathematics Genetic marker Taxonomy (biology) [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM] [SDE.BE]Environmental Sciences/Biodiversity and Ecology Software |
| Zdroj: | Bioinformatics Bioinformatics, 2020, 36 (21), pp.5264-5266. ⟨10.1093/bioinformatics/btaa657⟩ Bioinformatics, Oxford University Press (OUP), In press, ⟨10.1093/bioinformatics/btaa657⟩ |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | Motivation Phylogenetic placement (PP) is a process of taxonomic identification for which several tools are now available. However, it remains difficult to assess which tool is more adapted to particular genomic data or a particular reference taxonomy. We developed Placement Evaluation WOrkflows (PEWO), the first benchmarking tool dedicated to PP assessment. Its automated workflows can evaluate PP at many levels, from parameter optimization for a particular tool, to the selection of the most appropriate genetic marker when PP-based species identifications are targeted. Our goal is that PEWO will become a community effort and a standard support for future developments and applications of PP. Availability and implementation https://github.com/phylo42/PEWO. Supplementary information Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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